Eric J. N. Vilain

The paper introduces Watershed-DL, a framework integrating sequence-to-omics predictions and multi-omics data to prioritize rare variants, finding it increases prioritized variants by 61.4% and identifies candidate disease alleles.

This study evaluates the diagnostic yield of long-read genome sequencing in cases where short-read sequencing failed, finding an incremental yield of 4.7% due to LR-GS's ability to detect structural variants and other complex genomic features.

The paper introduces a data model and dataset for rare disease research, enabling interoperable multi-omic data integration across clinical sites.

duoNovo identifies de novo variants from parent-proband duos using long-read sequencing, achieving high precision and low error rates in diagnostic evaluations.

Genome sequencing identifies pseudoexons as a common cause of Mendelian disease, with some variants missed by prior exome testing.

The paper identifies mitochondrial DNA variants in undiagnosed rare disease families using exome and genome sequencing data, leading to diagnoses in 0.4% of cases.

The paper develops Paraphase, a HiFi-based method to resolve highly similar paralogous genes, revealing genetic diversity and de novo events in segmental duplications.

This paper uses long-read sequencing to comprehensively identify pathogenic variants in the CYP21A2 locus for Congenital Adrenal Hyperplasia, including phasing and module counts, improving diagnostic accuracy.

This study evaluates the diagnostic yield of long-read nanopore sequencing in rare disease detection, finding it covers more genes and detects additional variants compared to short-read sequencing.

Mostly de novo variants in an 18 bp constrained region of U4 snRNA gene RNU4-2 cause a syndromic neurodevelopmental disorder, estimated to explain 0.41% of cases.

The PING Consortium builds a genomic data repository to study genetic modifiers of prenatal viral infections' effects on brain development and neurodevelopmental outcomes.

This study benchmarks long-read genome alignment tools for human genomics, finding that no single tool resolves all structural variants, and recommends using multiple tools for comprehensive analysis.

This paper compares traditional and chatbot-based consent processes for genomics research, finding shorter consent times and positive participant feedback with the chatbot.

The paper identifies DNA methylation and gene expression differences in the hypothalamus of rams with different sexual partner preferences, finding three genes associated with sexual behaviors.

The paper identifies DNA methylation changes linked to cyanogenic cassava exposure and konzo in Sub-Saharan Africa.

The paper develops a method to deconvolve cell-type mixtures using enhancer-promoter methylation profiles from long-read data, achieving higher accuracy than promoter-based approaches.

The paper identifies a novel SARS-CoV-2 spike variant, S:N679S, in a neonatal patient and finds it present in other samples from the US mid-Atlantic region.

The paper identifies mutation-specific pathophysiological mechanisms in SATB1 variants causing distinct neurodevelopmental disorders.

nanotatoR annotates structural variants using OGM data, providing comprehensive information for pathogenicity assessment and variant prioritization.

This study identifies DHX37 variants as a novel molecular cause of 46,XY gonadal dysgenesis, particularly in embryonic testicular regression syndrome.

The paper develops a method to detect diploid-triploid mixoploidy using whole genome sequencing data and validates it with clinical cytogenetic testing.